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Hi all,
quite a basic question, but I find they can be the hardest to find answers for.
If I have transcripts with greater level of expression (measured by FPKM), can I have more confidence in the result if they are found differentially expressed? I am using edgeR under common dispersion model (with counts, not FPKM, to be clear; not ideal, I know, but at the end of the day we want genes potentially impacting a biological system in vivo and <100 appear when tagwise dispersion is used). Also I understand that 'more confidence' will be derived by using a stricter method, please humour me and my question
References to this end (either for or agin!) would be great.
quite a basic question, but I find they can be the hardest to find answers for.
If I have transcripts with greater level of expression (measured by FPKM), can I have more confidence in the result if they are found differentially expressed? I am using edgeR under common dispersion model (with counts, not FPKM, to be clear; not ideal, I know, but at the end of the day we want genes potentially impacting a biological system in vivo and <100 appear when tagwise dispersion is used). Also I understand that 'more confidence' will be derived by using a stricter method, please humour me and my question
References to this end (either for or agin!) would be great.